Gene loci information

Transcript annotation

  • This transcript has been annotated as Cytochrome P450 CYP12A2.

Parent gene

Gene structure

  • The exon-intron structure of all isoforms are indicated below. CDS regions are colored in green. TSS and TTs that were predicted with CTR-Seq data are indicated in solid circle and squares, respectively. More specific data are shown in the table below.

Chromosome Gene Transcript Category ID Start End
chr_3 g1688 g1688.t2 TSS g1688.t2 12558295 12558295
chr_3 g1688 g1688.t2 isoform g1688.t2 12558361 12559668
chr_3 g1688 g1688.t2 exon g1688.t2.exon1 12558361 12558633
chr_3 g1688 g1688.t2 cds g1688.t2.CDS1 12558361 12558633
chr_3 g1688 g1688.t2 exon g1688.t2.exon2 12558688 12558793
chr_3 g1688 g1688.t2 cds g1688.t2.CDS2 12558688 12558793
chr_3 g1688 g1688.t2 exon g1688.t2.exon3 12558884 12559007
chr_3 g1688 g1688.t2 cds g1688.t2.CDS3 12558884 12559007
chr_3 g1688 g1688.t2 exon g1688.t2.exon4 12559056 12559331
chr_3 g1688 g1688.t2 cds g1688.t2.CDS4 12559056 12559331
chr_3 g1688 g1688.t2 exon g1688.t2.exon5 12559391 12559547
chr_3 g1688 g1688.t2 cds g1688.t2.CDS5 12559391 12559547
chr_3 g1688 g1688.t2 exon g1688.t2.exon6 12559606 12559668
chr_3 g1688 g1688.t2 cds g1688.t2.CDS6 12559606 12559668
chr_3 g1688 g1688.t2 TTS g1688.t2 12559652 12559652

Sequences

>g1688.t2 Gene=g1688 Length=999
ATGTTCATACGACAATCATTATCAACTACTCGTCGATTATTTTCGACAAATTTTGCAAAT
GAACTTCAAGAAGCAAAACCATTTTCTCAAATTCCTAAAATATCAGCTTTAAAATTAGTT
ATGGGTAATTTACCTGGTGGGAAATATTACAAGAAGTCAATAAAAGATATTCAAGATATG
TTTTATAAAGAATATGGTTGCATTGTAAAAATGCCGGGACTTTTTGGTCAACCTGAAATG
ATTTTTACCTTCAATGCAGACGATTTTGAAAAAGCATTCAGAGCAGAAGGAATTTGGCCA
GTGAGATTTGGAATTGAAACTTTAAAACATTATAGAGAAACAATGCGTCCAGAAATTTAT
ACAGAATTTGGAAGTTTAGGAACAAGTGATGGACAGAAATGGCAAACAACTAGAACAATT
GTCAATCCAATCATGATGCAACCTAAAACTGTCAAATTTTATACTCAACAAATTGATGAA
ATTGCTAAAGAACTTGTTGAAATAATGAGAAATATAAAAAATGATAAAAATGAAATGCCA
GGTAATTTCAGTGACTACCTCAATAGATGGTCGCTTGAATCAATTGCAACGATTGCAGTA
GAAAAACGATTAAATGTTCTTAGCGGTAAAACTGACGATGAAAATAGTAAAAAATTGATC
AAAGTCATTAGACAATTTTTCGAGCAAGGACCAGAATTTGAAGGAAAGCCAAGTATTTGG
AAGTATTATGAAACCAAAGATTTTAAGAATCTTATAGAAGTTTATGACACTATGACGAGT
ATTGTTTTCAATTATGTGAATGAAGCCATCAAAAGATTTGAAACAGAAGAAGTCAAAGAA
GGTCAGGAAGAAAGCATTTTGAGGAAGCTTTTAAAAGTTAATAAAAATGTGGCATTTATC
ACTGCTAGTGATTTATTAATTGCTGGTGTTGATACTACCGCTTCCGGTGTCACATTCATA
CTTTATTTATTAGCAAAAAATCCAGAAAAACAAGAAAAA

>g1688.t2 Gene=g1688 Length=333
MFIRQSLSTTRRLFSTNFANELQEAKPFSQIPKISALKLVMGNLPGGKYYKKSIKDIQDM
FYKEYGCIVKMPGLFGQPEMIFTFNADDFEKAFRAEGIWPVRFGIETLKHYRETMRPEIY
TEFGSLGTSDGQKWQTTRTIVNPIMMQPKTVKFYTQQIDEIAKELVEIMRNIKNDKNEMP
GNFSDYLNRWSLESIATIAVEKRLNVLSGKTDDENSKKLIKVIRQFFEQGPEFEGKPSIW
KYYETKDFKNLIEVYDTMTSIVFNYVNEAIKRFETEEVKEGQEESILRKLLKVNKNVAFI
TASDLLIAGVDTTASGVTFILYLLAKNPEKQEK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
6 g1688.t2 Coils Coil Coil 151 178 -
5 g1688.t2 Gene3D G3DSA:1.10.630.10 Cytochrome p450 22 333 1.6E-57
2 g1688.t2 PANTHER PTHR24291:SF155 CYTOCHROME P450 301B1 26 333 7.1E-57
3 g1688.t2 PANTHER PTHR24291 CYTOCHROME P450 FAMILY 4 26 333 7.1E-57
1 g1688.t2 Pfam PF00067 Cytochrome P450 38 333 4.9E-25
8 g1688.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 304 -
9 g1688.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 305 325 -
7 g1688.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 326 333 -
4 g1688.t2 SUPERFAMILY SSF48264 Cytochrome P450 40 333 2.36E-29

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

GO terms from InterProScan

GOID TERM ONTOLOGY
GO:0020037 heme binding MF
GO:0016705 oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen MF
GO:0005506 iron ion binding MF
GO:0055114 NA NA

KEGG

Orthology

This gene did not have any KEGG ortholog annotations (KAAS, GHOSTZ).

Expression

Transcript expression in Pv11 cells

TPM values are indicated as average +/- STDEV.

Differential expression

Differentially expressed genes were identified with DESeq2 using the ‘run_DE_analysis.pl’ script from Trinity. Transcripts were determined as differentially expressed when (1) FDR < 0.05 (2) fold change > 2 (TPM calculated by RSEM). DE information and fold change between conditions are indicated in the plot below. There were no conditions that were differentially expressed